Can we test the omnigenic theory with empirical data in Poplar? Approach: Build gene networks from transcriptomic data to define core genes Complex traits prediction Quantitative and Population genetics of gene expression with respect to their position in the network
240 genotypes from 11 P. nigra natural populations Two common garden experiments (RCBD, 6 blocks): ORL (Fr) SAV (It) Contrasted growth conditions:
ORL design, June 2015 (4th year of growth) Cambium and Xylem on 480 trees (2 biol. reps. in 2 blocks) \(\rightarrow\) 960 RNA samples Equimolar pooling of RNA per tree Sequencing @ POPS transcriptomic platform Illumina HiSeq 2000, Single-Read 10 samples / lane \(\rightarrow\) \(\sim 20\) million reads / sample Mapping on P. trichocarpa v3.0 41,335 primary transcripts \(\rightarrow\) read counts Data cleaning pipeline: Filter out transcripts with 0 count in any sample (n = 1,653) 39,682 transcripts : Normalization (TMM) Variance stabilization (\(log_2(n+1)\)) Building a gene network R package WGCNA (Langfelder & Horvath, 2008) Defining Gene Subsets Module membership (\(KME\)) provides a measure of connectivity within the network Three \(KME\) based gene subsets (\(n = 3,968\) - \(10 \%\)) Core Peripheral Random One ‘statistically important’ subset (\(n = 635\)) Boruta (Kursa & Rudnicki 2010) Which Genes Matter to Predict Complex Traits? R package h2o (Kraljevic, 2018) Two constrasted prediction models Which Genes Matter to Predict Complex Traits? Core and Peripheral Gene Subsets Differ Depending on the Prediction Model Used –> Core and Peripheral Gene Subsets Differ According to their Genetic Features Summary Acknowledgements V Jorge, O Rogier (INRA BioForA, Orléans) V Brunaud, ML Martin Magniette, C Paysant-Leroux, L Soubigou-Taconnat (POPS transcriptomic platform @ IPS2, Saclay) ANR - SYBIOPOP project (ANR-13-JSV6-0001)
Module membership (\(KME\)) provides a measure of connectivity within the network Three \(KME\) based gene subsets (\(n = 3,968\) - \(10 \%\)) Core Peripheral Random One ‘statistically important’ subset (\(n = 635\)) Boruta (Kursa & Rudnicki 2010)
V Jorge, O Rogier (INRA BioForA, Orléans) V Brunaud, ML Martin Magniette, C Paysant-Leroux, L Soubigou-Taconnat (POPS transcriptomic platform @ IPS2, Saclay) ANR - SYBIOPOP project (ANR-13-JSV6-0001)